You can not over-filter...at least it won't do any harm. The most harm would come from spending too much money on a giant filter
The whisper 60 should hold plenty of bacteria, and do plenty of aeration at the same time. (air stones just look pretty, they don't really aerate much).
Did you just change the filter cartridges? Change them as little as possible. Really just rinse them out and replace the charcoal, but only do one side per week.
Do you have the water level too high? Bring the water to just past the decorative rim on the tank (put another way: as low as possible without the waterline visible from outside). You want the water to cascade into the tank. I've found that bringing the water up too high after water change can cause the tank to go cloudy and smell foul.